The flat panel display industry has been attempting to employ inkjet printing to manufacture display devices, and in particular, color filters for flat panel displays. Because the pixel wells into which ink is deposited when printing patterns for color filters may be particularly small, the possibility of printing error is significant. Thus, it is frequently necessary to inspect substrates to ensure that ink has been properly deposited. Therefore, efficient methods and apparatus for inspecting inkjet printed substrates and making adjustments to printing parameters are desirable.